Lotus Land Story is a straightforward shoot'em-up, except that the player controls a flying girl instead of the typical spacecraft. When enemies are shot down, they may drop various "items", such as Power Ups, Point items or other special items with various effects. The game consists of 6 stages, each stage having a mid-boss and an end-of-stage boss.

In Lotus Land Story, the player can choose between playing the characters Reimu Hakurei (shrine maiden) or Marisa Kirisame (witch). Both character can choose between 2 shot types, resulting in 4 combinations.

Base system / Power ups
The player starts at (fire) power 0. Enemies might drop red Power Up items when shot. Collecting power up items raises the power by 1, gradually increasing the damage that the shots do.
As the Power goes up, so does the number of bullets the player fires.
Once the player reaches Max Power, the red items will slowly increase the points they yield, starting with 10 and slowly doubling up to a certain max.

Base system / Extra lives
Extra lives are earned when the player reaches a certain score.

Base system / Boss attack patterns and "Spell Cards"
Bosses in Project Shrine Maiden usually have several "attack patterns", following each other. The boss starts with the first, and if the player reduces the boss's health bar by a certain amount, the boss switches to the next attack pattern. A typical early stage boss can have about 3 attack patterns, with the final bosses closer to 10.
Clearing the boss attacks without dying or bombing yields the player a bonus.

High score system in Lotus Land Story
Adding to the basic system from The Story of Eastern Wonderland, where the Point Items give more points the higher up on screen they are collected (up to a maximum of 51,200), Lotus Land Story features a Dream value, that starts at 0. Collecting Dream items, raises the Player's Dream by 1,000, to a max of 12,800. When collecting a Point Item, the Dream value is simply added to the points gained, so after 5 Dream items collected, the points gained for collecting a Point item would vary between 5,000 and 56,200 instead of between 0 and 51,200.

Also, once the player has reached Max Power, the red Power up items will start yielding substantial points.

High score aiming summary:
Apart from the obvious of collecting point items, aiming for high score in Lotus Land story roughly consists of collecting the Dream items when they appear, and not dying, as that will reset the points gained from red Power up items.